FOXBOROUGH — It wasn’t just the game the Patriots lost against the 49ers Sunday night — they also likely lost the No. 2 playoff seed in the AFC and the extra week of rest and preparation that comes with it.

The Patriots will likely be the third seed, behind Houston and Denver, with the fourth, fifth, and sixth seeds still up in the air.

The Broncos’ win in Baltimore Sunday combined with New England’s loss allowed Denver to move up to the second spot, which the Patriots (10-4) had been holding since Week 13. Denver is 11-3.

In order for the Patriots to overtake the Broncos, they would have to win out and Denver would have to lose one of its final two games. The Patriots would then get the No. 2 seed on head-to-head result.

But 5-9 Cleveland and 2-12 Kansas City both travel to Denver, and neither poses a strong challenge to Peyton Manning and his new team, at least on paper.

If one were going to upset the Broncos, it would more likely be the Browns, who started the season 0-4 but have gone .500 since. They have had wins over AFC North foes Pittsburgh and Cincinnati, both of which are still in the playoff hunt.

The Patriots travel to Jacksonville Sunday and close out the regular season at home against the Dolphins.

On Monday, the Patriots said there’s nothing they can do now about having lost that coveted No. 2 position.

“We’re not worried about that right now,” Vince Wilfork said. “We’ve got two games left; the last thing we’re thinking about now is seeding.”

Safety Steve Gregory said much the same after the game.

“We come out every week and we work hard all week to win a football game, and when you don’t win, that’s disappointing,” he said. “The seeding and all that will play out how it plays out. We’ve still got a few games left here, so we’ll just grind away and get on the next game.”

Another hope that the Patriots could land a bye could be getting the top seed. Currently Houston is 12-2, with a home game against Minnesota Sunday and a road game in Indianapolis to finish its schedule.

Were the Texans to lose both games, the Broncos to lose one, and the Patriots to win both of theirs, all three would finish 12-4.

In that scenario, far-fetched though it may be, New England would get the No. 1 seed by virtue of its wins against both Denver and Houston.

If, as the odds would suggest, New England remains the third seed, it would host a wild-card game the weekend of Jan. 6. Right now, that opponent would be the Bengals, but the AFC North titlist has not been determined and Baltimore, Cincinnati, and Pittsburgh are all still in the running.

The Ravens clinched a playoff berth Sunday despite their loss.

There is also the chance that New England might prefer being the fourth seed to get a more favorable matchup. We’ve seen that happen before, in 2005, when Matt Cassel played the final three quarters of the finale against Miami, and New England lost.

The Patriots slipped to the fourth seed, and hosted and drubbed the Jaguars in the opening round before falling to Denver on the road a week later.

Having to play in the wild-card round is not a kiss of death: five of the last seven Super Bowl champions had to play on the opening weekend of the postseason. Only the Steelers (2008) and Saints (2009) won it all with a first-round bye.

Regardless of the permutations, the Patriots are professing to do what they do best: look only at the game right in front of them.

“We just have to get back to doing things the way we know how to do it. It starts on the practice field: prepare, prepare well and execute well,” Wilfork said. “That’s what it comes back to. We’re going to take this game [in Jacksonville] just like any other game.

“We’re going to move on after this, make the corrections and move on. That’s all you can do.”